通过上述的两个测试集,结果虽然不期待能做到完全分离,但结构预测模型的输出plddt,pAE以及预测结构的RMSD都能有效提升binder的辨别率。 3. ProteinMPNN-FR助力binder设计 3.1 引入新的pAE filter助力筛选 为了验证两个Filter方法对实验成功率的影响,作者对4个靶点受体蛋白进行binder设计,使用的依然是标准RIFDock流程,共...
将第一阶段中,看起来比较靠谱的那些binder取出进行进一步地优化,具体的做法是将受体的序列和binder的序列用200个氨基酸的gap进行相连,然后一同预测整个复合物的结构,并且在反向传播的只优化binder自身的序列; 在优化的过程中,只用了motif的loss,从而来保证binder大致结合在受体的某个区间内,不施加hallucination, repulsive...
The polypeptide shows a specific binding for C-reactive protein (CRP). The utilization of the polypeptide in assays for determining the concentration of CRP is described. The purification of CRP, and compositions comprising the CRP also are provided.BALTZER LARS...
et al. Improving de novo protein binder design with deep learning. Nat. Commun. 14, 2625 (2023). CAS PubMed PubMed Central ADS Google Scholar Glasscock, C. J. et al. Computational design of sequence-specific DNA-binding proteins. Preprint at bioRxiv https://doi.org/10.1101/2023.09....
designbinderproteinpyrosettaalphafold2 UpdatedApr 6, 2025 Python prody/ProDy Star468 A Python Package for Protein Dynamics Analysis pythondynamicsprotein UpdatedMar 21, 2025 Python Efficient pythonic random access to fasta subsequences pythonbioinformaticsgenomicsindexingdnaproteinfastasamtoolsbgzf ...
Binder, D. Salyakina, A. Erhardt, M. Ising, P.G. Unschuld, N. Kern, S. Lucae, T.M. Brueckl, M.B. Mueller, B. Fuchs, B. Puetz, R. Lieb, M. Uhr, F. Holsboer, B. Mueller-Myhsok, M.E. Keck Association of a Met88Val diazepam binding inhibitor (DBI) gene polymorphism ...
Why risk matters for protein binder design [arXiv:2504.00146] Systematic comparison of Generative AI-Protein Models reveals fundamental differences between structural and sequence-based approaches [bioRxiv 2025.03.23.644844] • [code] • [Supplementary] Deep Learning-Driven Protein Structure Predicti...
R. et al. Improving de novo protein binder design with deep learning. Nat. Commun. 14, 2625 (2023). Article ADS CAS PubMed PubMed Central Google Scholar Wu, F., Jing, X., Luo, X. & Xu, J. Improving protein structure prediction using templates and sequence embedding. Bioinformatics ...
An allele-specific tagging system that uses a protein of interest (POI) fused to a FKBP12(F36V) construct that allows specific degradation of the fused POI via an FKBP12(F36V) binder linked to a cereblon (CRBN) or a von Hippel–Lindau (VHL) ligand. Bio-orthogonal chemistry A chemical ...
The combination of synthetic binders has already been described as a strategy to improve the affinity for a target; examples include fluorescent proteins51, anti-EGFR VHHs52, a PDZ domain binder53,54, or even kinases with 10FN3-derived binders35. Our aim here was different, although the final...